Sunday, February 27, 2011

Well, this could be fun. Next week I am making a guest appearance in a Writing class at UC Davis. The class focuses on writing in Biology and the instructor invited me to come in as a guest to coordinate a discussion of the arsenic paper and the coverage of it.

When the instructor asked for reading assignments I said they should read:

Saturday, February 26, 2011

For those interested in what the US Government is doing in areas relating to microbiology, there is a useful site to check out called "The Microbe Project". The goal of this project is to "to maximize the opportunities offered by genome-enabled microbial science to benefit science and society, through coordinated interagency efforts to promote research, infrastructure development, education and outreach." There is a lot of information there on different agencies and their funding opportunities.

Sunday, February 20, 2011

Well, just got back from a very brief trip to give a talk at UCSF. I was invited by graduate students via the following email message

The students in the DeRisi Lab at UCSF are thrilled to invite you as our selection for the California Institute for Quantitative Biosciences (QB3) and Integrative Program in Quantitative Biology (iPQB) Invitational Speaker Series! This is a new type of speaker series at UCSF where students from a laboratory directly nominate and invite speakers from outside UCSF to deliver lectures about cutting-edge topics in quantitative biology. All nominations are discussed by a QB3/iPQB student committee, and a speaker list is compiled from many outstanding nominations. The invited speakers are scientists who gathered especially strong support from their nominating lab and the QB3/iPQB student committee, and who have an outstanding record in delivering exciting research talks grounded in quantitative methods. As our selected nominee, your travel, lodging and food expenses will be covered by funds from QB3/iPQB.

It was impossible to say no - I am always thrilled to be invited by student groups. It took a bit to coordinate when I would come (I am notoriously bad at planning and answering such invitations). But eventually, with a little prodding, I answered and we picked a date. I of course then asked to change the date and we settled on February 17.

Personally, I am a bit skeptical of the LGT claim because most of the evidence they present relies on amplification (ie PCR). But without getting into too many of the details myself I thought I would just post some background reading connected to some of my past work in this area for anyone interested in this type of thing

Information about claim of HGT into humans from bacteria that was in the Lander et al Human Genome paper:

Well, it seems that the Sequence Read Archive (SRA) is going away sometime in the near future. I posted about the SRA last week and in the discussion someone posted an email message that supposedly was from David Lipman of the NCBI saying that the SRA is going to be closing. This has now been confirmed and I thought I would just post some links discussing this

Tuesday, February 15, 2011

A few days ago I got a message that made a big impact on my publication record in PubMed Central. My number of publications there went up by 85 in one fell swoop (see below for the list ...). Did I publish 85 new papers yesterday? No. But a journal in which I have been a co-author on many papers recently finally showed up in Pubmed Central. The journal is called Standards in Genomic Sciences. The journal's scope is:

The goal of SIGS is to serve as an open-access, standards-supportive publication for rapid dissemination of concise genome and metagenome reports that comply with the emerging MIGS/MIMS standards, detailed standard operating procedures, meeting reports, reviews and commentaries, data policies, white papers and other gray literature that is relevant to genome sciences but currently absent from the scholarly literature.

Lots of jargon, I know. But you can ignore that. The reason I am writing here is that this journal is a place to publish what could be called "genome sequencing data reports." These reports are a way for data producers to describe, in a formal manner, their sequencing project - and to share - in a formal manner - not only the data but also metadata about the organism(s) sequenced and the methods used. As sequencing gets cheaper and easier, we need places for people to publish these types of "data papers" to both produce a citable unit with a DOI relating to the data, and to also share the details of the data production in a way that a simple Genbank entry does not.

One aspect of the papers in this "SIGS" journal is that they are being done in a way that is compliant with sets of standards for sharing metadata about the organism and the project. I confess, when I first heard about these standards developments, I was bored almost to tears. But now I realize that this is a very important aspect of getting the most out of genome data. If people who sequence a genome not only release the sequence data, but also a table of information about the project, such as information about the organism (e.g., aerobic vs anaerobic, location of isolation) and about the data production (e.g., sequencing methods used) then people will be able to do high throughput analyses of these features. Then we will not just be looking at sequence but also connecting these sequences to organismal features. Right now that is very hard to do since genome data is rarely accompanied by machine usable information about the organism that has been sequenced.

Today I am writing to recognize the people connected to this movement - the people who created the standards, the people who created and run the journal, and the people writing papers for this journal. All of them are to be commended for their vision and their dedication to openness. Thus I am giving George Garrity the EIC of SIGS my "Open Access Pioneer Award" for creating SIGS, making it an open access journal, for keeping it running and for getting its papers into Pubmed Central and soon Pubmed. Many others should be recognized too for their contribution to SIGS (see the whole list of founding members here). I also should recognize Nikos Kyrpides from the DOE JGI who helped coordinate the writing and submission of these papers along with Hans Peter Klenk from the DSMZ. Without them, these papers would never have gotten out there. Plus I think some credit goes to Michigan State University and the Department of Energy which apparently are sponsors of SIGS

However, one database from NCBI is driving me a bit wacky these days. This is the Sequence Read Archive (SRA). Known to some as the "Short Read Archive" this database is supposedly for storing "sequencing data from the next generation of sequencing platforms including Roche 454 GS System®, Illumina Genome Analyzer®, Life Technologies AB SOLiD System® , Helicos Biosciences Heliscope®;, Complete Genomics®, and Pacific Biosciences SMRT®."

It certainly seems to be used for that function. But alas, storing sequence is not the only need here. Recovering sequence and making use of it is really the key. And this is the area I have been having trouble with (especially related to environmental studies like rRNA PCR and metagenomics). Rather than go on about my particular issues here (and thus possibly biasing the discussion too much), I am wondering what others think of the SRA? Usability? Ease of deposition? Ease of extraction? Missing features? Things it does or does not do well? Do we need a new system for environmental projects?

Any and all comments welcome here or on twitter or on Friendfeed or wherever. See Friendfeed stream below:

Well, one reason is that it had been unavailable outside of the TIM paywall. However, the author, Mark Pallen, with a little prodding from me, managed to get the Editors to feature it as a "free" article on their website for at least some time. So everyone, download this paper and distribute it to as many as you can (legally). Oh, and read it, it is definitely worth a read.

In the article Pallen argues for giving mitochondria their own family w/in bacteria. I think that would be a good idea as they are really just a highly reduced form of bacteria. We give endosymbionts, even those with tiny genomes, their own groups. So why note organelles that are derived from bacteria? After all - phylogenetically they are bacteria.

Pallen even goes so far as to suggest rethinking of mitochondria as bacteria will help with efforts to engineer mitochondria in various ways. That is an interesting notion.

I suppose one could push this to an extreme position and argue that the nucleus and all the genes associated with it are really just a shell around a mitochondrial core. And then I guess all eukaryotes could be considered bacteria. But I do not want to confuse the issue too much here. Overall, I really really like this paper. I wish it were in an OA journal, but since it is free for now I think it is worth checking out. In the long run, it would be better (hint hint Mark Pallen) to publish such thought provoking pieces in places everyone can access ....

So I guess this paper, along with all the "microbiome" stuff means that humans are really just carrying vessels for bacteria.

Panel members representing different approaches will give short informal presentations (10 minutes each), to be followed by active audience participation (this all following traditional pizza and beer, of course!).

Confirmed Panel Members:

Tracy Heath

Pat Holroyd

Nick Matzke (moderator)

Sarah Werning

The venerable Biosystematists group (http://www.biosystematists.org/), operating since 1936 (see the history on the website), is the only inter-institutional seminar/discussion group on evolution for the Bay Area, so we encourage everyone to join in.

Friday, February 04, 2011

Just thought I would give people the heads up - I am helping plan a session on "Microbiology of the Indoor Environment" that will happen at the "Indoor Air 2011" meeting in Austin, TX June 5-10 2011. The conference itself covers an enormous amount of ground about, well, Indoor Air. And I am helping the meeting organizer Rich Corsi plan a special session that will try to bring together (1) researchers working on culture-independent studies of the microbes in the indoor environment with (2) scientists and engineers and others who work on the indoor environment. Will post more about this special session as details come out. But thought I would give people a heads up ...

I note, this is a component of the Sloan Foundation's New program in Indoor Microbiology - I have received a grant from them to create something called microBEnet ("microbiology of the Built Environment network"). In this microBEnet project we will be working to foster communication, collaboration, research and other related activities for the Sloan Program. More coming on microBEnet soon but if you want a little taste (a very preliminary taste) - see our blog here.

The paper is from Eshel-Ben Jacob and colleagues from many institutions around the world.

Here is a summary of the article (from the paper)

Background

The pattern-forming bacterium Paenibacillus vortex is notable for its advanced social behavior, which is reflected in development of colonies with highly intricate architectures. Prior to this study, only two other Paenibacillus species (Paenibacillus sp. JDR-2 and Paenibacillus larvae) have been sequenced. However, no genomic data is available on the Paenibacillus species with pattern-forming and complex social motility. Here we report the de novo genome sequence of this Gram-positive, soil-dwelling, sporulating bacterium.

Results

The complete P. vortex genome was sequenced by a hybrid approach using 454 Life Sciences and Illumina, achieving a total of 289× coverage, with 99.8% sequence identity between the two methods. The sequencing results were validated using a custom designed Agilent microarray expression chip which represented the coding and the non-coding regions. Analysis of the P. vortex genome revealed 6,437 open reading frames (ORFs) and 73 non-coding RNA genes. Comparative genomic analysis with 500 complete bacterial genomes revealed exceptionally high number of two-component system (TCS) genes, transcription factors (TFs), transport and defense related genes. Additionally, we have identified genes involved in the production of antimicrobial compounds and extracellular degrading enzymes.

Conclusions

These findings suggest that P. vortex has advanced faculties to perceive and react to a wide range of signaling molecules and environmental conditions, which could be associated with its ability to reconfigure and replicate complex colony architectures. Additionally, P. vortex is likely to serve as a rich source of genes important for agricultural, medical and industrial applications and it has the potential to advance the study of social microbiology within Gram-positive bacteria.

The main idea behind this is to look at social communication strategies as a measure of intelligence. And from a genomics point of view one can measure the genetic diversity of genes likely involved in these processes. Such counting of genes is not the most useful thing in the world but more important, these organisms really have some fascinating behaviors and in the end we should measure behavior diversity not genomic diversity of putative social genes to measure "bacterial IQ".

A friend/colleague Peter Turnbaugh just sent me a note about a new metagenomics book which he contributed to (see Metagenomics: Current Innovations and Future Trends). So I sniffed around Amazon and found a collection now of books that focus heavily on metagenomics. I do not know much about the quality of them but some look interesting. So I created a mini-Amazon collection of them: Metagenomics Books. Yet another sign metagenomics is still hot I suppose ...

In this paper, which is pretty cool, the authors make use of digitized books to track and study cultural trends. The data is f#*$#$ impressive. The results are very very interesting. The press coverage was very positive. The word, however, was and is awful. Did they really really have to call it culturomics, thereby contaminating their fascinating work with all the baggage of genomics? Really? Really? For that you get a Bad Omics Word of the Day Award.

Anyway - here are some links to coverage of the culturomics work, which as I said, is quite impressive. Just wish they had come up with their own non omicy word: